rs10849441
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001384598.1(PLEKHG6):c.1525-23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 1,589,732 control chromosomes in the GnomAD database, including 166,781 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.40 ( 12926 hom., cov: 32)
Exomes 𝑓: 0.46 ( 153855 hom. )
Consequence
PLEKHG6
NM_001384598.1 intron
NM_001384598.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.255
Genes affected
PLEKHG6 (HGNC:25562): (pleckstrin homology and RhoGEF domain containing G6) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Located in cell junction and centrosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHG6 | NM_001384598.1 | c.1525-23A>G | intron_variant | ENST00000684764.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHG6 | ENST00000684764.1 | c.1525-23A>G | intron_variant | NM_001384598.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.397 AC: 60251AN: 151694Hom.: 12919 Cov.: 32
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GnomAD3 exomes AF: 0.414 AC: 102975AN: 248920Hom.: 22407 AF XY: 0.417 AC XY: 56189AN XY: 134738
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GnomAD4 exome AF: 0.456 AC: 655064AN: 1437920Hom.: 153855 Cov.: 28 AF XY: 0.454 AC XY: 325359AN XY: 716776
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GnomAD4 genome ? AF: 0.397 AC: 60273AN: 151812Hom.: 12926 Cov.: 32 AF XY: 0.400 AC XY: 29658AN XY: 74144
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at